QIIME2 Amplicon occupies 15GB on disk, so you don’t really want each user installing it in their own home directory because of the amount of space that multiple parallel installations will consume. It also takes a long time to install, which is not as pleasant a user experience as having it already there for immediate use.<\/p>\n\n\n\n
The following guide is written using a Debian system. The only step that ought to differ between Debian-like and RedHat-like systems is the first step: installing Conda itself.<\/p>\n\n\n\n
Become root, then follow along with https:\/\/conda.io\/projects\/conda\/en\/latest\/user-guide\/install\/rpm-debian.html<\/a> to add the Miniconda package repository to your computer and then run Create \/opt\/conda\/.condarc containing:<\/p>\n\n\n\n Fetch the Conda environment definition for QIIME2 Amplicon: Once you are happy: Test the QIIME2 installation by dropping back into an unprivileged account and following the Users’ guide below.<\/p>\n\n\n\n Start with: I am not a bioinformaticist so I cannot help you there. https:\/\/docs.qiime2.org\/2024.5\/<\/a> has some tutorials.<\/p>\n","protected":false},"excerpt":{"rendered":" QIIME2 Amplicon occupies 15GB on disk, so you don’t really want each user installing it in their own home directory because of the amount of space that multiple parallel installations will consume. It also takes a long time to install, which is not as pleasant a user experience as having it already there for immediate … Continue reading “Multi-user Conda environments: a worked example installing QIIME2 Amplicon”<\/span><\/a><\/p>\n","protected":false},"author":1447,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[3,18],"tags":[],"class_list":["post-254","post","type-post","status-publish","format-standard","hentry","category-gnulinux","category-python"],"_links":{"self":[{"href":"https:\/\/blogs.ncl.ac.uk\/helengriffiths\/wp-json\/wp\/v2\/posts\/254","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.ncl.ac.uk\/helengriffiths\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.ncl.ac.uk\/helengriffiths\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/helengriffiths\/wp-json\/wp\/v2\/users\/1447"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/helengriffiths\/wp-json\/wp\/v2\/comments?post=254"}],"version-history":[{"count":11,"href":"https:\/\/blogs.ncl.ac.uk\/helengriffiths\/wp-json\/wp\/v2\/posts\/254\/revisions"}],"predecessor-version":[{"id":271,"href":"https:\/\/blogs.ncl.ac.uk\/helengriffiths\/wp-json\/wp\/v2\/posts\/254\/revisions\/271"}],"wp:attachment":[{"href":"https:\/\/blogs.ncl.ac.uk\/helengriffiths\/wp-json\/wp\/v2\/media?parent=254"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/helengriffiths\/wp-json\/wp\/v2\/categories?post=254"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/helengriffiths\/wp-json\/wp\/v2\/tags?post=254"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}apt install conda<\/code>.<\/p>\n\n\n\n2: Share the multi-user environments with your users<\/h3>\n\n\n\n
channels:\n - defaults\npkg_dirs:\n - \/shared\/conda\/pkgs\n - $HOME\/.conda\/pkgs\nenvs_dirs:\n - \/shared\/conda\/envs\n - $HOME\/.conda\/envs<\/code><\/pre>\n\n\n\n3: Install QIIME2 Amplicon<\/h3>\n\n\n\n
wget https:\/\/data.qiime2.org\/distro\/amplicon\/qiime2-amplicon-2024.5-py38-linux-conda.yml<\/code> then review qiime2-amplicon-2024.5-py38-linux-conda.yml to make sure that it’s going to behave benignly towards your system.<\/p>\n\n\n\nconda env create -p \/opt\/conda\/envs\/qiime2-amplicon-2024.5 --file qiime2-amplicon-2024.5-py38-linux-conda.yml<\/code> and wait for a long time. The use of -p<\/code> differs from the official QIIME2 installation instructions and is the “special sauce” that puts the QIIME2 environment into a shared location, \/opt\/conda\/envs, instead of \/root\/.conda\/envs. <\/p>\n\n\n\nUsers’ guide<\/h2>\n\n\n\n
My sysadmin installed QIIME2. How do I access it?<\/h3>\n\n\n\n
source \/opt\/conda\/etc\/profile.d\/conda.sh<\/code>. You can put that in your .bashrc\/.zshrc\/whatever-your-profile-file-is-called to run every time you login.<\/p>\n\n\n\nconda env list<\/code> should get you a list containing qiime2-amplicon-2024.5 and the following should show you some information about your QIIME2 installation:<\/p>\n\n\n\nconda activate qiime2-amplicon-2024.5\nqiime info<\/code><\/pre>\n\n\n\nHow do I use QIIME2?<\/h3>\n\n\n\n